178 Open source projects that are alternatives of or similar to sunbeam

Monitor computational workflows in real time

Bonsai: Fast, flexible taxonomic analysis and classification

Fast in-silico normalization algorithm for NGS data

Reproducible Research with Rmarkdown: data management, analysis, and reporting all-in-one

Snakemake based pipeline for RNA-Seq analysis

Public scenarios to crowdsource experiments (such as DNN crowd-benchmarking and crowd-tuning) using Collective Knowledge Framework across diverse mobile devices provided by volunteers. Results are continuously aggregated at the open repository of knowledge:

A toolbox for writing Sweave or other LaTeX-based papers and reports and to prettify the output of various estimated models.

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Manager for multi-container computing environments

Short course on the targets R package

Documentation of the Snakemake-Workflows project

Collective Knowledge repository with actions to unify the access to different predictive analytics engines (scipy, R, DNN) from software, command line and web-services via CK JSON API:

Open Plant Pathology website

Metagenomics/viromics pipeline that focuses on automation, user-friendliness and a clear audit trail. Jovian aims to empower classical biologists and wet-lab personnel to do metagenomics/viromics analyses themselves, without bioinformatics expertise.

gargammel is an ancient DNA simulator

Creating virtual environments for R.

Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

A workflow for creating small NGS test data sets, useful for continuous integration.

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your personal computer!

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

creating optimal conditions for reproducibility

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

A setup script to generate ITK Python Wheels

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.

ATAC-seq snakemake pipeline

Coding Standards for the USC Biostats group

Strain-level abundances estimation in metagenomic samples using variation graphs

⛔ ARCHIVED ⛔

Code for "Depth Uncertainty in Neural Networks" (https://arxiv.org/abs/2006.08437)

🐍 Snakefiles for common RNA-seq data analysis workflows.

No description or website provided.

From genomes to phenotypes: Traitar, the microbial trait analyzer

Meta-Omics Software for Community Analysis

An easy-to-use way for running Galaxy workflows.

Platform for integrating genomic analysis with Jupyter Notebooks.

Kervolution implementation using TF2.0

A Deep Learning Approach to Ultrasound Image Recovery

Unifying Variational Autoencoder (VAE) implementations in Pytorch (NeurIPS 2022)

Remove contaminated contigs from genomes using k-mers and taxonomies.

📦 Create a package or compendium structure

Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/, https://github.com/DerrickWood/kraken).

Framework for Analysis of Class-Incremental Learning with 12 state-of-the-art methods and 3 baselines.

Empirical Software Engineering journal (EMSE) open science and reproducible research initiative

Reproducible R Scripts Via Date Controlled Installing & Loading of CRAN & Git Packages

Cross-disease comparison of case-control gut microbiome studies

MaAsLin2: Microbiome Multivariate Association with Linear Models

The GenePattern Server web application

The uncompromising Snakemake code formatter

A library for creating and curating reproducible pipelines for scientific and industrial machine learning

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

Close assembly gaps using long-reads at high accuracy.

WRENCH: Cyberinfrastructure Simulation Workbench

Deploy a BinderHub from scratch on Microsoft Azure

ganon classifies short DNA sequences against large sets of genomic sequences efficiently, with download and update of references (RefSeq/Genbank), taxonomic (NCBI/GTDB) and hierarchical classification, customized reporting and more

Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data

Fully reproducible, open source scientific articles in LaTeX.

ukbREST: efficient and streamlined data access for reproducible research of large biobanks

Guide for Reproducible Research and Data Science in Jupyter Notebooks